2-133286621-G-T

Variant names:

• chr2-133286621-G-T
• rs13412008
• NM_207363.3:c.143+16416C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_207363.3(NCKAP5):​c.143+16416C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.15 in 152,122 control chromosomes in the GnomAD database, including 1,715 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.15 (1715 hom., cov: 32)
• Consequence: NCKAP5 NM_207363.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.133
• Publications: 3 publications found

Genes affected

NCKAP5 (HGNC:29847): (NCK associated protein 5) Predicted to be involved in microtubule bundle formation and microtubule depolymerization. Predicted to be active in microtubule plus-end. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NCKAP5	NM_207363.3	c.143+16416C>A		intron_variant	Intron 4 of 19	ENST00000409261.6	NP_997246.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NCKAP5	ENST00000409261.6	c.143+16416C>A		intron_variant	Intron 4 of 19	5	NM_207363.3	ENSP00000387128.1
NCKAP5	ENST00000427594.5	c.128+16416C>A		intron_variant	Intron 2 of 4	1		ENSP00000399070.1
NCKAP5	ENST00000409213.5	c.143+16416C>A		intron_variant	Intron 4 of 17	5		ENSP00000386952.1
NCKAP5	ENST00000358991.4	c.143+16416C>A		intron_variant	Intron 3 of 3	5		ENSP00000351882.4

Frequencies

GnomAD3 genomes AF: 0.150 AC: 22828 AN: 152004 Hom.: 1709 Cov.: 32

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.0850

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.142

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.152

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.150 AC: 22871 AN: 152122 Hom.: 1715 Cov.: 32 AF XY: 0.149 AC XY: 11088 AN XY: 74368

African (AFR) AF: 0.170 AC: 7063 AN: 41504

American (AMR) AF: 0.154 AC: 2357 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.120 AC: 417 AN: 3466

East Asian (EAS) AF: 0.138 AC: 714 AN: 5168

South Asian (SAS) AF: 0.143 AC: 686 AN: 4804

European-Finnish (FIN) AF: 0.121 AC: 1286 AN: 10596

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.146 AC: 9914 AN: 67992

Other (OTH) AF: 0.154 AC: 326 AN: 2114

Alfa AF: 0.152 Hom.: 289

Bravo AF: 0.154

Asia WGS AF: 0.161 AC: 559 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	4.8
DANN	Benign	0.58
PhyloP100		-0.13
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13412008; hg19: chr2-134044193;